In England’s second innings, Stokes was bizarrely lbw playing no shot to spinner Noman Ali.
England were ultimately skittled for 112, their lowest total in Pakistan, setting the hosts towards a nine-wicket win.
“He is disappointed, naturally,” said McCullum. “We all know how competitive and driven the skipper is. He’ll be hurting right now with how the series has unfolded.
“That injury was quite significant. He had to put in a lot of graft and subconsciously maybe you’re not quite as screwed down as you can be in terms of decision-making. That’s natural.”
England have a short turnaround to their next tour, a three-Test series in New Zealand beginning at the end of November.
A squad is expected to be announced in the coming days, with few changes anticipated.
Leg-spinner Rehan Ahmed is likely to make way, possibly for a batter or wicketkeeper to cover for Jamie Smith, who will miss part or all of the tour for the birth of his first child.
The first Test is in Christchurch, the city where Stokes was born before moving to the UK at the age of 12.
“He’ll be better for the run, no doubt,” said McCullum, himself a New Zealander.
“It will be a couple of weeks off, freshen up and back to conditions which are a bit more similar to England. It’s another opportunity for us.”